Just set up the new rig and did a few slews. After pushing "go home", the mount heads back alright but the Dec portion does not line up with the lower body (about 2 deg out)... is this normal, or should I be concerned?
I think you are OK. "Home" is an arbitrary location for the mount and need not be precise. Consider an older mount that required a manual move to "home". What does need to be more accurate is repeatability. Try sending it home several times from various positions. If it goes to the same location each time, you will be fine.
bobequus "Home" is an arbitrary location for the mount and need not be precise.... What does need to be more accurate is repeatability.
Be mindful though that this true home position (probably an internal index mark, like on an RST-135) is the one that you should use to level your mount. Not the external visible index mark.